Interpretive Summary: Samples of the plant pathogen Phytophthora infestans, the cause of the potato famine in the mid 1800s, present in dried leaf lesions were collected from potato and tomato tissue that has been stored in herbaria since the time of the famine. DNA from these lesions was sequenced and compared to DNA sequence data collected from modern strains of the pathogen to help clarify the origin of the strains that caused the historical famine.

Technical Abstract:
Potato late blight, caused by the oomycete Phytophthora infestans, is a plant pathogen of historical dimension that remains one of the world’s most destructive crop diseases. Ever since its first global outbreak of the 1840s that culminated in the Great Famine in Ireland, late blight has been a major threat to potato production. Until a few decades ago, P. infestans genetic diversity outside of Mexico, the center of origin of the pathogen and its hosts, was very low, and one scenario held that a single genotype, US-1, had dominated the global P. infestans population for 150 years. This was subsequently challenged, based on the analysis of three SNPs in the mitochondrial DNA of herbarium specimens from the nineteenth century. To resolve this controversy, we have compared the genomes of 11 herbarium samples with 15 modern strains. We conclude that the nineteenth century epidemic was caused by a unique genotype, HERB-1, that persisted for at least 50 years. While HERB-1 is distinct from all examined modern isolates, it is related to the US-1 genotype that replaced it in the global population early in the twentieth century. We propose that these two pandemic genotypes emerged from a single metapopulation that was established in the early 1800s outside of the species’ Mexican center of diversity, possibly in North America.